\contentsline {chapter}{FIGURES}{v}{chapter*.2}
\contentsline {chapter}{{CHAPTER\ 1: INTRO}}{1}{chapter.1}
\contentsline {section}{\numberline {1.1}Overview}{1}{section.1.1}
\contentsline {section}{\numberline {1.2}Bioinformatics Web Portals}{1}{section.1.2}
\contentsline {section}{\numberline {1.3}Bioinformatics Pipelines}{2}{section.1.3}
\contentsline {section}{\numberline {1.4}Rare Codon Analysis}{2}{section.1.4}
\contentsline {chapter}{{CHAPTER\ 2: BIOCOMPUTE: Principles and Architecture of a Bioinformatics Web Portal}}{4}{chapter.2}
\contentsline {section}{\numberline {2.1}Introduction}{4}{section.2.1}
\contentsline {section}{\numberline {2.2}System Goals}{5}{section.2.2}
\contentsline {section}{\numberline {2.3}Data-Action-Queue}{6}{section.2.3}
\contentsline {section}{\numberline {2.4}System Interface Implementation}{8}{section.2.4}
\contentsline {subsection}{\numberline {2.4.1}Data}{9}{subsection.2.4.1}
\contentsline {subsection}{\numberline {2.4.2}Action}{10}{subsection.2.4.2}
\contentsline {subsection}{\numberline {2.4.3}Queue}{10}{subsection.2.4.3}
\contentsline {subsection}{\numberline {2.4.4}System Description}{11}{subsection.2.4.4}
\contentsline {subsection}{\numberline {2.4.5}Biocompute Modules}{11}{subsection.2.4.5}
\contentsline {subsection}{\numberline {2.4.6}Sharing Work Across Machines}{14}{subsection.2.4.6}
\contentsline {subsubsection}{\numberline {2.4.6.1}Crawler}{15}{subsubsection.2.4.6.1}
\contentsline {subsubsection}{\numberline {2.4.6.2}Using Work-Queue's Catalog Server}{16}{subsubsection.2.4.6.2}
\contentsline {subsection}{\numberline {2.4.7}Data Management for BLAST}{16}{subsection.2.4.7}
\contentsline {subsection}{\numberline {2.4.8}Performance of Data Management Schemes}{18}{subsection.2.4.8}
\contentsline {subsection}{\numberline {2.4.9}Social Challenges of Biocompute}{20}{subsection.2.4.9}
\contentsline {section}{\numberline {2.5}Related Work}{21}{section.2.5}
\contentsline {section}{\numberline {2.6}Conclusions}{22}{section.2.6}
\contentsline {chapter}{{CHAPTER\ 3: Pipelines for Bioinformatics Computing}}{25}{chapter.3}
\contentsline {section}{\numberline {3.1}Introduction}{25}{section.3.1}
\contentsline {section}{\numberline {3.2}Microsatellite Pipeline}{25}{section.3.2}
\contentsline {subsection}{\numberline {3.2.1}Introduction}{25}{subsection.3.2.1}
\contentsline {subsection}{\numberline {3.2.2}Pipeline Description}{26}{subsection.3.2.2}
\contentsline {subsection}{\numberline {3.2.3}Performance}{26}{subsection.3.2.3}
\contentsline {section}{\numberline {3.3}Ka/Ks pipeline}{26}{section.3.3}
\contentsline {subsection}{\numberline {3.3.1}Introduction}{26}{subsection.3.3.1}
\contentsline {subsection}{\numberline {3.3.2}Pipeline Description}{27}{subsection.3.3.2}
\contentsline {subsection}{\numberline {3.3.3}Transcriptomics Challenges}{27}{subsection.3.3.3}
\contentsline {subsubsection}{\numberline {3.3.3.1}Existing Solutions}{27}{subsubsection.3.3.3.1}
\contentsline {subsubsection}{\numberline {3.3.3.2}Novel Solution}{28}{subsubsection.3.3.3.2}
\contentsline {subsubsection}{\numberline {3.3.3.3}Design}{28}{subsubsection.3.3.3.3}
\contentsline {subsubsection}{\numberline {3.3.3.4}Results}{29}{subsubsection.3.3.3.4}
\contentsline {subsection}{\numberline {3.3.4}Performance}{29}{subsection.3.3.4}
\contentsline {section}{\numberline {3.4}Practical Difficulties}{29}{section.3.4}
\contentsline {subsection}{\numberline {3.4.1}Evil Magic Numbers}{29}{subsection.3.4.1}
\contentsline {subsection}{\numberline {3.4.2}Encapsulation}{29}{subsection.3.4.2}
\contentsline {subsection}{\numberline {3.4.3}Lessons Learned}{29}{subsection.3.4.3}
\contentsline {chapter}{{CHAPTER\ 4: RARECODONS}}{31}{chapter.4}
\contentsline {section}{\numberline {4.1}Abstract}{31}{section.4.1}
\contentsline {section}{\numberline {4.2}Introduction}{32}{section.4.2}
\contentsline {section}{\numberline {4.3}Methods}{36}{section.4.3}
\contentsline {subsection}{\numberline {4.3.1}pre-processing}{36}{subsection.4.3.1}
\contentsline {subsection}{\numberline {4.3.2}Peak Method}{36}{subsection.4.3.2}
\contentsline {subsection}{\numberline {4.3.3}Poisson Sampling}{36}{subsection.4.3.3}
\contentsline {subsection}{\numberline {4.3.4}Limitation of Poisson}{38}{subsection.4.3.4}
\contentsline {subsection}{\numberline {4.3.5}Holistic Evaluation of Rare Codon Co-Occurrence}{39}{subsection.4.3.5}
\contentsline {subsection}{\numberline {4.3.6}Comparison Measures}{39}{subsection.4.3.6}
\contentsline {subsubsection}{\numberline {4.3.6.1}n99}{41}{subsubsection.4.3.6.1}
\contentsline {subsubsection}{\numberline {4.3.6.2}skew}{41}{subsubsection.4.3.6.2}
\contentsline {subsubsection}{\numberline {4.3.6.3}solomon}{41}{subsubsection.4.3.6.3}
\contentsline {subsubsection}{\numberline {4.3.6.4}kurtosis}{41}{subsubsection.4.3.6.4}
\contentsline {subsubsection}{\numberline {4.3.6.5}Correlation of Comparison Measures}{42}{subsubsection.4.3.6.5}
\contentsline {subsection}{\numberline {4.3.7}Controlling for GC-content}{42}{subsection.4.3.7}
\contentsline {subsection}{\numberline {4.3.8}Visualization}{42}{subsection.4.3.8}
\contentsline {section}{\numberline {4.4}Results}{44}{section.4.4}
\contentsline {subsection}{\numberline {4.4.1}Performance}{44}{subsection.4.4.1}
\contentsline {subsection}{\numberline {4.4.2}Biological Results}{44}{subsection.4.4.2}
\contentsline {chapter}{{CHAPTER\ 5: CONCLUSION AND FUTURE WORK}}{46}{chapter.5}
\contentsline {section}{\numberline {5.1}Future Work}{46}{section.5.1}
\contentsline {subsection}{\numberline {5.1.1}Improvements to Biocompute}{46}{subsection.5.1.1}
\contentsline {subsection}{\numberline {5.1.2}Future Rare Codon Work}{46}{subsection.5.1.2}
\contentsline {section}{\numberline {5.2}Conclusions}{46}{section.5.2}
